Hmm... What about this:
Allow Humans to spawn holographic (thus NOT collision-based! You can walk through them!) projections of buildings. They can do this at S2, at which point a hologram will cost as much as the building it replicates, and at S3, at which point they cost only half the cost of the original building... Or maybe at S2 the costs should be a bit lower...
Holograms act as follows:
Holograms are not collidable: you can walk through them.
If an alien comes close to a hologram, the hologram will go partially translucent with a blue-ish hue.
If a Human touches a hologram, the hologram will go partially translucent, too.
Whenever a power surge occurs, a hologram will go translucent for a few milliseconds. Power surges occur when:
1) An alien attacks a Human building
2) Humans build buildings
3) Humans build holograms (power surge twice as long as a normal power surge)
4) There is no power at the hologram (infinitely long power surge)..
Making a holographic Reactor will cost 20 build points, by the way..

As for aliens: I'm not sure. Maybe it'd be nice if you'd let them build 'fleshy pods'. Basically, a pod is a fleshy membrane filled with acid and fleshy goo, which once it is ruptured (destroyed) gets spread out like regular alien building explosions, hurting humans, but only a little (5hp max?).
Fleshy pods should be insanely cheap (2BP? maybe more?), fast to build and come in various colours and sizes, which are randomly chosen to ensure extreme 'chaos' in a Fleshy-pod infested Alien base. So basically, fleshy pods make it hard for humans to walk through an alien base (they need to jump more often) and they obscure alien buildings a bit because there are SO MANY buildings on the screen, which makes it hard to notice what buildings you should target.
Fleshy pods should be killable by 1/4th of a Rifle clip. They're weak.
